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- PDB-2e3h: Crystal structure of the CLIP-170 CAP-Gly domain 2 -

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Basic information

Entry
Database: PDB / ID: 2e3h
TitleCrystal structure of the CLIP-170 CAP-Gly domain 2
ComponentsRestin
KeywordsSTRUCTURAL PROTEIN / CAP-Gly / Cytoplasmic linker / tubulin binding
Function / homology
Function and homology information


microtubule plus-end binding / microtubule bundle formation / intermediate filament / RHO GTPases activate IQGAPs / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule organization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / positive regulation of microtubule polymerization / ruffle ...microtubule plus-end binding / microtubule bundle formation / intermediate filament / RHO GTPases activate IQGAPs / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule organization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / positive regulation of microtubule polymerization / ruffle / Resolution of Sister Chromatid Cohesion / tubulin binding / RHO GTPases Activate Formins / cytoplasmic vesicle membrane / kinetochore / Separation of Sister Chromatids / microtubule cytoskeleton / mitotic cell cycle / cell cortex / microtubule binding / microtubule / centrosome / zinc ion binding / identical protein binding / nucleus / cytosol
Similarity search - Function
CLIP1, zinc knuckle / CLIP1 zinc knuckle / CAP Gly-rich-like domain / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / SH3 type barrels. ...CLIP1, zinc knuckle / CLIP1 zinc knuckle / CAP Gly-rich-like domain / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
CAP-Gly domain-containing linker protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMaesaki, R. / Hakoshima, T.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural basis for tubulin recognition by cytoplasmic linker protein 170 and its autoinhibition
Authors: Mishima, M. / Maesaki, R. / Kasa, M. / Watanabe, T. / Fukata, M. / Kaibuchi, K. / Hakoshima, T.
History
DepositionNov 26, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Restin


Theoretical massNumber of molelcules
Total (without water)9,6811
Polymers9,6811
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.937, 54.937, 57.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-18-

HOH

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Components

#1: Protein Restin / CLIP-170 / Cytoplasmic linker protein 170 alpha-2 / Reed- Sternberg intermediate filament- ...CLIP-170 / Cytoplasmic linker protein 170 alpha-2 / Reed- Sternberg intermediate filament-associated protein / Cytoplasmic linker protein 1


Mass: 9681.208 Da / Num. of mol.: 1 / Fragment: CAP-Gly domain 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLIP-170 / Plasmid: pGEX4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P30622
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MAC Science DIP-2040 / Detector: IMAGE PLATE / Date: Feb 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 17953 / % possible obs: 98.9 % / Rsym value: 0.042 / Net I/σ(I): 44.3
Reflection shellResolution: 1.45→1.56 Å / Mean I/σ(I) obs: 11.5 / Rsym value: 0.107 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LPL

1lpl


Resolution: 1.45→47.67 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 0.922 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21483 915 5.1 %RANDOM
Rwork0.19168 ---
obs0.19281 17032 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.472 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0.11 Å20 Å2
2---0.22 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.45→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms651 0 0 119 770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022663
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.969891
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.281579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.72522.75929
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25315124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.419156
X-RAY DIFFRACTIONr_chiral_restr0.0920.2100
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02485
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.2275
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.2437
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.297
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2211.5413
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8492652
X-RAY DIFFRACTIONr_scbond_it2.4643279
X-RAY DIFFRACTIONr_scangle_it3.5744.5239
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.451→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 68 -
Rwork0.199 1262 -
obs--99.92 %

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